Ammonia Capture in Rhodium(II)-Based Metal–Organic Polyhedra via Synergistic Coordinative and H-Bonding Interactions

Ammonia (NH3) is among the world’s most widely produced bulk chemicals, given its extensive use in diverse sectors such as agriculture; however, it poses environmental and health risks at low concentrations. Therefore, there is a need for developing new technologies and materials to capture and store ammonia safely. Herein, we report for the first time the use of metal–organic polyhedra (MOPs) as ammonia adsorbents. We evaluated three different rhodium-based MOPs: [Rh2(bdc)2]12 (where bdc is 1,3-benzene dicarboxylate); one functionalized with hydroxyl groups at its outer surface [Rh2(OH-bdc)2]12 (where OH-bdc is 5-hydroxy-1,3-benzene dicarboxylate); and one decorated with aliphatic alkoxide chains at its outer surface [Rh2(C12O-bdc)2]12 (where C12O-bdc is 5-dodecoxybenzene-1,3-benzene dicarboxylate). Ammonia-adsorption experiments revealed that all three Rh-MOPs strongly interact with ammonia, with uptake capacities exceeding 10 mmol/gMOP. Furthermore, computational and experimental data showed that the mechanism of the interaction between Rh-MOPs and ammonia proceeds through a first step of coordination of NH3 to the axial site of the Rh(II) paddlewheel cluster, which triggers the adsorption of additional NH3 molecules through H-bonding interaction. This unique mechanism creates H-bonded clusters of NH3 on each Rh(II) axial site, which accounts for the high NH3 uptake capacity of Rh-MOPs. Rh-MOPs can be regenerated through their immersion in acidic water, and upon activation, their ammonia uptake can be recovered for at least three cycles. Our findings demonstrate that MOPs can be used as porous hosts to capture corrosive molecules like ammonia, and that their surface functionalization can enhance the ammonia uptake performance.


S2. Computational methods
Density Functional Theory Calculations. All calculations were carried out using the Gaussian 16 program revision B.01. 5 We employed density functional theory (DFT) method at the M06-L/SDD level of theory. We selected the M06-L hybrid functional of Truhlar and Zhao because of its broad accuracy for metallochemical calculations for all metals. 6 Previous calculations of metalorganic paddlewheel structures in vacuo comparing different DFT functionals and basis sets with MP2 ab initio quantum chemistry calculations showed that MP06 is the best performing functional irrespective of the basis set employed (energies and geometrical quantities such as bond distances and angles calculated with this functional show little dependence on the specific basis set employed). 7 For our calculations, we selected the commonly used SDD basis set because it is suitable for both Rh(II) and acetate. It combines double zeta with the Stuttgart-Dresden ECP, which reduces the cost caused by a large number of electrons, giving close agreement with experimental results. 8

Molecular Dynamics
Simulations. All MD simulations were performed using the NAMD program, version 1.14. 9 The species included in the simulations are ammonia molecules in gas phase and a single Rh-MOP (H-RhMOP, OH-RhMOP or OMe-RhMOP) fixed in the center of the simulation box. In order to simplify the calculation, the atomic positions of the MOP were fixed during the simulations and only NH3 molecules were allowed to move. The force field employed in the simulation was a modification of the CHARMM force field to include Rh interactions as determined by our DFT calculations, as described below. The initial structures for the simulations were prepared as follows. First, we start building the atomic coordinates of the Rh-MOPs based on the experimental single crystal crystallographic information. 2 The structures were [Rh2(H-bdc)2]12 , [Rh2(OH-bdc)2]12 and [Rh2(OMe-bdc)2]12 for the cases of H-RhMOP, OH-RhMOP and OMe-RhMOP respectively (where H-bdc is 1,3-benzenedicarboxylate, OH-bdc is 5-hydroxy-1,3-benzenedicarboxylate and OMe-bdc is 5-methoxy-1,3-benzenedicarboxylate). Then, ammonia molecules were introduced randomly distributed around the Rh-MOPs without contact. We considered several simulations with different simulation box sizes in order to model different NH3 densities which correspond to different points of the adsorption isotherm. In all cases, before running the actual MD simulations, we performed an energy minimization to correct any possible bad contacts between atoms. In the MD simulations we solved the Newton equations of motion using a time step of 2 fs. Electrostatic interactions were computed using the PME method with the standard settings in NAMD (1 Å resolution, updated each 2 time steps). Lennard-Jones interactions were truncated at 1.2 nm employing a switching function starting at 1.0 nm. Periodic boundary conditions were employed in all directions. The temperature was fixed at 298 K using the Langevin thermostat (relaxation time 1 ps). The simulations were performed for times between 10-50 ns time depending on each case. The simulation times were selected monitoring the number of adsorbed molecules and ensuring that this quantity has equilibrated.    Note that OH-RhMOP shows a higher percentage of weight loss before decomposition (ca. 300ºC). This is attributed to its highly hydrophilic character that makes it uptake atmospheric water before the TGA measurement.
S-9 Figure S5. Ammonia-adsorption (solid dots) and -desorption (outlined dots) at 298 K of pristine activated H-RhMOP (black); H-RhMOP after the first NH3-adsorption isotherm activated under vacuum (blue); and H-RhMOP after the first NH3-adsorption isotherm activated under vacuum and heat (130º C). The NH3 uptake was normalized per mol of Rh(II) site in H-RhMOP. For this calculation, the molecular weight of H-RhMOP (6405 g/mol) was considered.  S-12

S5.1. DFT calculations of the interaction between Rh2(Ac)4 and NH3
Instead of the full Rh(II) paddlewheel cluster (which is too big for DFT calculations), we considered rhodium acetate [Rh2(Ac)4] as a surrogate and different numbers of NH3 molecules. We performed a geometry optimization in 4 different cases, corresponding to [Rh2(Ac)4] and 1, 2, 3 and 4 NH3 molecules, as seen in Figure S6. The optimized structures obtained for the four different simulations showed that Rh(II)-paddlewheel can interact with ammonia through two different interactions: coordinative (1 NH3 molecule per Rh(II) site) and through H-bonding (up to 3 NH3 molecules per Rh(II) site). The binding energy of the Rh-NH3 coordination bond was found as follows: Using Equation 1, we obtain a value of -31.75 Kcal/mol for the Rh-N coordination bond.
The interaction energy of the systems, in which there are Rh(II)-coordinated NH3 molecules and H-bonded NH3 molecules, was determined as follows:  Table S2 shows that each addition of NH3 to the Rh2(Ac)4(NH3) complex is stabilized by ca. -10 Kcal/mol, which is good agreement with the stabilizing energy generally provided by H-bonding interactions.
Overall, the final configuration for the system with 4 NH3 molecules per Rh(II)-paddlewheel cluster showed high stabilization energy and symmetry. In the most stable configuration, one NH3 molecule is coordinated to the axial Rh(II) site and 3 NH3 molecules are H-bonded to the Rh2(Ac)4(NH3). The H-bonded NH3 molecules are distributed at 120º between each, as shown in Figure S7.

S5.1.2. DFT calculations of the interaction between Rh2(Ac)4, NH3 and H2O
In order to estimate the preference of the axial site of the Rh(II) paddlewheel for NH3 or H2O when the two molecules are simultaneously present, we have simulated the situation in which a Rh(II) paddlewheel is exposed simultaneously to one H2O and one NH3 molecule. In this simulation, H2O and NH3 molecules were initially located in symmetric positions from the Rh(II) paddlewheel ( Figure S10a). Next, the geometry optimization algorithm was used to identify the minimum energy configuration, which corresponded to the situation in which NH3 molecules occupy the axial site coordination site ( Figure S10a). This result suggests that Rh(II)-MOPs can be efficient adsorbents for ammonia even in the presence of moisture.

S5.2.1. Parametrization of the Force Field from DFT calculations
The force field employed for the molecules was based on the standard CHARMM force field, 28,29 but the parameters for the force field were modified to account for: (i) the Rh-N interaction not parametrized in the force field; and (ii) the fact that simulations take place in the gas phase (and CHARMM partial charges are derived for simulations in solvent). In general, in CHARMM force field, one includes inter-molecular nonbonding interactions given by electrostatic and Lennard-Jones 12-6 potentials and bonded interactions including harmonic bonds, angle and dihedral potentials. In our simulations, the atoms of Rh-MOP were maintained at fixed positions, and the N-H bonds in the NH3 molecule were considered fixed so bonded interactions were not needed in our simulations. For the electrostatic and Lennard-Jones interactions, we employed the following parameters. The charges in all the atoms were determined from the DFT calculations described before using Bader charges, and they are compiled in Table S4. For the Lennard-Jones interactions, we employed the standard atom types and parameters, as defined in CHARMM. In the case of Rh (not defined in standard version of CHARMM), we employed previously proposed Lennard-Jones parameters (Rmin= 1.3575 Å and ε= -1.973 kcal/mol) 30 31 combined with standard mixing rules of CHARMM for cross interactions, except for the case of the Rh-N interaction. In that case, we parametrized the Lennard-Jones parameters to reproduce the energies and bond distances obtained in our DFT calculations. The parametrization was done in an iterative way as follows. The Rh2(Ac)4 structure with one NH3 molecule considered in DFT calculations was now considered in NAMD in an energy minimization calculation using the above mentioned parameters for all atoms and an initial guess for the Rh-N Lennard-Jones parameters (Rmin and ε). The Rh-N bond energy was calculated from the forcefield with NAMD using a protocol analogous to that employed in DFT (see Equation 1). The obtained values of interaction energy and Rh-N bond distance were compared to DFT and the force field parameters were modified until the comparison with DFT attained a prescribed tolerance. After this optimization protocol, the obtained parameters for the Rh-N Lennard-Jones interaction were Rmin=2.20 Å and ε=-26.587 Kcal/mol. Using the final parametrization of the force field, the obtained interaction energy and bond distances were E(Rh-N)= -31.75 Kcal/mol and d(h-N)=2.20 Å, which match the DFT values.

S5.2.2. Molecular dynamic simulations of the interaction between H-RhMOP and NH3
We run four different MD simulations to examine the interaction between H-RhMOP and NH3. All of these simulations had one H-RhMOP in the middle of the simulation box and the same number of NH3 molecules (457 molecules) inside the simulation box. The difference between the four simulations (named as System 1 to System 4) was the size of the simulation box, which was used to replicate the increase in NH3 pressure that occurs during the experimental adsorption isotherm. System 1 with 400 Å 3 ; System 2 with 161 Å 3 ; System 3 with 100 Å 3 and System 4 with 80 Å 3 .
The interaction of NH3 with H-RhMOP was monitored through the radial distribution function acquired for each of the simulations (Figure S8). It was observed that the peak attributed to H-bonding interactions increases with the pressure of the system, whereas the Rh-N coordination remains at the same arbitrary intensity through the different simulations. From this data, it can be concluded that high NH3 pressure favors the H-bonding interactions whereas the Rh-N coordination occurs even at low NH3 pressure. The number of adsorbed ammonia molecules were calculated for each system (Table S5), by counting the number of NH3 molecules contributing to the first peak in the radial distribution function (i.e. to consider a NH3 molecule as an adsorbed molecule, the Rh-N distance has to be smaller than 2.5 Å). A similar criterion was applied to identify H-bonded NH3 molecules. In that case, the Rh-N distance is 4.5 Å. The numerical analysis of the interacting NH3 molecules per H-RhMOP in each system simulated seems to indicate that System 3 is the one that is closest to the most stable configuration with ca. 4 NH3 molecules per Rh(II) site. System 4 presents a slightly higher amount of NH3 loading but at the expense of destabilizing H-bonding network of NH3 molecules on top of each Rh(II) site as evidenced by the longer H-bonding distances found in this case ( Figure S9).   S-24

S9.1 OH-RhMOP and NH3
The same protocol employed for the molecular dynamic simulations of H-RhMOP and NH3 was also employed for OH-RhMOP and NH3 with the following results (Figures S15 and S16). We used the same simulation box, parameters and atoms to calculate the radial distribution function than H-RhMOP (see S5.  A close inspection of the configurations obtained for OH-RhMOP revealed the presence of additional interactions between ammonia and OH-RhMOP beyond the ones previously described for the Rh(II) paddlewheel cluster. Specifically, we found H-bonding interactions between the hydroxyl group of the OH-RhMOP and ammonia (i.e . OH···NH3), as depicted in Figure S17.

S-26
The number of adsorbed ammonia molecules were calculated for each system (Table S6), by counting the number of NH3 molecules contributing to the first peak in the radial distribution function (i.e. to consider a NH3 molecule as an adsorbed molecule, the Rh-N distance has to be smaller than 2.5 Å). A similar criterion was applied to identify H-bonded NH3 molecules. In that case, the Rh-N distance is 4.5 Å. For the case of OH···NH3 interaction, we considered a H···N distance of 2.5 Å. S-27

S10.1 C12-RhMOP and NH3
Considering that we did not obtain crystallographic structure for C12-RhMOP, we were not able to define the distribution of aliphatic chains in the MOP. To study the ability of oxygens from ether group to interact through H-bonding interactions, we used a simplified model to simulate the interaction of ether groups on the surface of Rh-MOPs with NH3. Specifically, we run the simulation of System 4 on a Rh-MOP functionalized on its surface with methoxy groups in order to check if an oxygen of an ether group is able to absorb or interact with ammonia molecules (Figure S18). Simulation box of 80 Å 3 and 57.1 molecules/nm 3 .